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Sulphate-Reducing Bacterial Diversity in a Calcareous Sandy Sediment Of DEPARTAMENTO DE MICROBIOLOGÍA Sulphate‐reducing bacterial diversity in a calcareous sandy sediment of Mallorca and community response to hydrocarbon contamination TESIS DOCTORAL Ana Belén Suárez Suárez Palma de Mallorca, 2012 The study was supported by the ECOSIP project (200530F0182‐200530F0183) funded by the CSIC, the FBBVA project BIOCON05/094, and the Spanish Ministry of Science and Innovation projects Consolider Ingenio 2010 CE‐CSD2007‐0005 and VEM2003‐0075‐C02‐01 (both co‐ financed with FEDER funding); additional funding was provided by the Max‐Planck Society and the Helmholtz Association. 2 Contents Resume ......................................................................................................................5 General Introduction..................................................................................................7 1. Anthropocene ‐ Mankind as a major geological force ............................................. 8 1.1. Fossil fuel consumption .............................................................................................................. 8 1.2. Petroleum composition .............................................................................................................. 9 1.3. Petroleum formation ................................................................................................................ 12 1.4. Environmental consequences of fossil fuel consumption ‐ hydrocarbon pollution in the marine environment ....................................................................................................................................14 1.5. Hydrocarbon pollution in the Mediterranean Sea.................................................................... 16 1.6. Fate and behaviour of the crude oil in the marine environment ............................................. 17 2. Ecological relevance of coastal ecosystems ........................................................... 19 2.1. Marine sediments ..................................................................................................................... 21 2.2. Carbonated sediments.............................................................................................................. 22 2.3. Coastal sandy sediments as biocatalytical filters...................................................................... 23 2.4. Dynamic ecology of sandy sediments....................................................................................... 24 2.5. Biogeochemical gradients in marine sediments ‐ Diversity of ecological niches......................25 3. Approaches in the study of microbial ecology in marine environments. .............. 33 3.1. Culture‐dependent techniques for the characterization of microbial communities................33 3.2. Direct enumeration of microorganisms in their environment.................................................. 34 3.3. Culture‐independent techniques for the characterization of microbial communities.............35 4. Background and aim of the thesis......................................................................... 41 5. References .............................................................................................................. 43 Experimental procedures .........................................................................................51 1. Sampling site........................................................................................................... 52 2. Mesocosms set up and sampling............................................................................ 53 3. Additional sampling................................................................................................ 55 4. Physico‐chemical features...................................................................................... 55 4.1. Sediment density, porosity and organic matter content.......................................................... 55 4.2. Pore water sulphate concentration .......................................................................................... 56 4.3. Sulphate reduction rates........................................................................................................... 56 5. Molecular biology approaches ............................................................................... 58 5.1. Sample manipulation ................................................................................................................ 58 5.2. DNA extraction from marine sandy sediment .......................................................................... 59 5.3. DNA extraction from enrichment cultures for metagenomic analyses .................................... 60 5.4. 16S rRNA gene clone libraries construction.............................................................................. 61 5.5. 16S rRNA gene sequence analyses and phylogenetic tree construction .................................. 62 5.6. Taxonomic classification of 16S rRNA and 23S rRNA gene fragments in the metagenome .....63 5.7. Taxonomic and functional metagenomic analysis.................................................................... 63 5.8. Quantification of total cell numbers by DAPI staining.............................................................. 64 5.9. Fluorescence in situ hybridization (FISH) .................................................................................. 65 6. Statistical diversity indexes .................................................................................... 68 3 7. Culture dependent approaches.............................................................................. 69 7.1. Artificial seawater medium for the cultivation of SRB.............................................................. 69 7.2. Most probable number dilution series ..................................................................................... 71 7.3. Establishment of hydrocarbon‐degrading enrichment cultures............................................... 72 7.4. Quantification of the sulphide production in the enrichment cultures.................................... 74 8. Analytical chemistry ............................................................................................... 74 8.1. Quantification of naphthalene in sediments by high performance liquid chromatography ....74 8.2. Gas chromatography................................................................................................................. 76 8.3. Ion cyclotron resonance Fourier transform mass spectrometry (ICR‐FT‐MS) analyses............77 9. References ............................................................................................................. 82 Chapter 1: Relevant environmental features of the ecosystem ................................86 1. Introduction............................................................................................................ 87 2. Results and discussion............................................................................................ 87 2.1. Environmental features ............................................................................................................ 87 2.2. Bacterial phylogenetic affiliation revealed by the 16S rDNA.................................................... 90 2.3. In situ quantification of the potential sulphate‐reducing bacteria fraction.............................. 93 2.4. Most probable number of culturable sulphate‐, iron‐ and manganese‐reducing bacteria in bare and vegetated sandy sediments.............................................................................................. 94 3. References .............................................................................................................. 96 Chapter 2: Response of sulphate‐reducing bacteria to an artificial oil spill in coastal Mediterranean marine sediment..............................................................................99 1. Introduction.......................................................................................................... 100 2. Results and discussion.......................................................................................... 100 2.1. Rationale of the experiment ...................................................................................................100 2.2. Changes in the microbial abundance after hydrocarbon contamination ...............................101 2.3. In situ sulphate reduction rates (SRR).....................................................................................104 2.4. Naphthalene quantification....................................................................................................105 2.5. Changes in the SRB culturability due to hydrocarbon contamination....................................106 2.6. Evidence of crude oil and PAH degradation by the SRB cultures............................................109 3. References ............................................................................................................ 113 Chapter 3: First insights into the phylogeny and physiology of Mediterranean SRB hydrocarbon degraders .......................................................................................... 114 1. Introduction.......................................................................................................... 115 2. Results and discussion.......................................................................................... 117 2.1. Establishment
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